melting.ionCorrection.magnesiumCorrections

Class Tan06MagnesiumCorrection

java.lang.Object

melting.correctionMethods.EntropyCorrection

melting.ionCorrection.magnesiumCorrections.Tan06MagnesiumCorrection

All Implemented Interfaces:

CorrectionMethod, NamedMethod

public class Tan06MagnesiumCorrection
extends EntropyCorrection
implements NamedMethod

This class represents the magnesium correction model tanmg06. It extends EntropyCorrection. Zhi-Jie Tan and Shi-Jie Chen, "Nucleic acid helix stability: effects of Salt concentration, cation valence and size, and chain length", 2006, Biophysical Journal, 90, 1175-1190.

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	aFormula
protected static String	bFormula
protected static String	entropyCorrection String entropyCorrection : formula for the entropy correction
protected static String	gFormula String gFormula : function associated with the electrostatic folding free energy per base stack.

Constructor Summary

Constructors

Constructor and Description
Tan06MagnesiumCorrection()

Method Summary

Methods

Modifier and Type	Method and Description
static double	computeFreeEnergyPerBaseStack(Environment environment) represents the function associated with the electrostatic folding free energy per base stack.
protected double	correctEntropy(Environment environment) corrects the computed entropy (delta S (Na = 1M)).
String	getName() Gets the full name of the method.
boolean	isApplicable(Environment environment) Check if the environment chosen by the user is a applicable with the correction model.

Methods inherited from class melting.correctionMethods.EntropyCorrection

correctMeltingResults

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

entropyCorrection

protected static String entropyCorrection

String entropyCorrection : formula for the entropy correction

aFormula

protected static String aFormula

bFormula

protected static String bFormula

gFormula

protected static String gFormula

String gFormula : function associated with the electrostatic folding free energy per base stack.

Constructor Detail

Tan06MagnesiumCorrection

public Tan06MagnesiumCorrection()

Method Detail

isApplicable

public boolean isApplicable(Environment environment)

Description copied from interface: CorrectionMethod

Check if the environment chosen by the user is a applicable with the correction model.

Specified by:

isApplicable in interface CorrectionMethod

Overrides:

isApplicable in class EntropyCorrection

Returns:

false if the correction method can't be used with the Environment. If the environment can make the results less reliable, a warning message will appear.

correctEntropy

protected double correctEntropy(Environment environment)

Description copied from class: EntropyCorrection

corrects the computed entropy (delta S (Na = 1M)).

Overrides:

correctEntropy in class EntropyCorrection

Returns:

double : corrected entropy;

computeFreeEnergyPerBaseStack

public static double computeFreeEnergyPerBaseStack(Environment environment)

represents the function associated with the electrostatic folding free energy per base stack.

Parameters:

environment -

Returns:

double g2 which represents the result of the function associated with the electrostatic folding free energy per base stack.

getName

public String getName()

Gets the full name of the method.

Specified by:

getName in interface NamedMethod

Returns:

The full name of the method.